VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Wed Apr 12 2023 - 09:30:56 CDT

Hi Dominique,

Is this the standard precompiled VMD downloaded from the UIUC site? If so, that usually ends poorly in my experience. In my lab, we compile VMD ourselves to use system python, with the rough outline of how to do this for newer Ubuntu versions (we use 22.04 in the lab) here: https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!9QtYGMZbAEbQjeMXWTB0luU5LNaaBkegTEhMHrhDmMicN7uSMAcpXBr8SYGIpUT35fRNXyL0Cq7P8AEpBjc$ . When you run vmd with -python, indeed some of the plugins that depend on tcl behave a bit weirdly, but for scripting use, either the user guide or the documentation for vmd-python (https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!9QtYGMZbAEbQjeMXWTB0luU5LNaaBkegTEhMHrhDmMicN7uSMAcpXBr8SYGIpUT35fRNXyL0Cq7PfuE7Q_0$ ) are usually pretty good for figuring out what you want to do.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Dominique Mias-Lucquin <dominique.mias-lucquin_at_loria.fr>
Date: Wednesday, April 12, 2023 at 9:58 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Python crash VMD1.9.4

Hello,
I'm trying to use the 1.9.4 version of VMD with python in Ubuntu 18.04.
I encountered several case:

  * vmd194 -python :
Info) VMD for LINUXAMD64, version 1.9.4a55 (October 18, 2021)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 40 CPUs, ISA dispatch enabled.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
Info) Free system memory: 7183MB (22%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator::
Info) [0] Quadro P620 4 SM_6.1 1.4 GHz, 2.0GB RAM SP32 KT AE2 ZC
Info) OpenGL renderer: Quadro P620/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture (4)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling OptiX shaders on 1 target GPU...
Info) Dynamically loaded 3 plugins in directory:
Info) /home/dominique/utils/vmd-1.9.4a55/bin/plugins/LINUXAMD64/molfile
after#0
Info) Starting Python...
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
'import site' failed; use -v for traceback
Segmentation fault

  * vmd194 then python: Work, but freeze the display windows until I exit. Nothing I do in python has an effect (molecule loading or drawing)

  * vmd194 then gopython: same as vmd194 -python

Does someone knows what append and how to fix it ?
Thank you very much,

Dominique MIAS-LUCQUIN.